Structure of PDB 8cgk Chain k Binding Site BS01

Receptor Information

>8cgk Chain k (length=144) Species: 679895 (Escherichia coli BW25113)

MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGF
EGGQMPLYRRLPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANI
IGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE

Ligand information

>8cgk Chain a (length=2699)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaaaacccgaugcaaacugcgaaua
ccggagaauguuaucacgggagacacacggcgggugcuaacguccgucgu
gaagagggaaacaacccagaccgccagcuaaggucccaaagucaugguua
agugggaaacgaugugggaaggcccagacagcgucgagucggccugcgcg
gaagauguaacggggcuaaaccaugcaccgaagcugcggcagcgacgcgu
uguuggguaggggagcguucuguaagccugcgaaggugugcugugaggca
ugcuggagguaucagaagugcgaaugcugacauaaguaacgauaaagcgg
gugaaaagcccgcucgccggaagaccaaggguuccuguccaacguuaauc
ggggcagggugagucgaccccuaaggcgaggccgaaaggcguagucgaug
ggaaacagguuaauauuccuguacuugguguuacugcgaaggggggacgg
agaaggcuauguuggccgggcgacgguugucccgguuuaagcguguaggc
ugguuuuccaggcaaauccggaaaaucaaggcugaggcgugaugacgagg
cacuacggugcugaagcaacaaaugcccugcuuccaggaaaagccucuaa
gcaucagguaacaucaaaucguaccccaaaccgacacagguggucaggua
gagaauaccaaggcgcuugagagaacucgggugaaggaacuaggcaaaau
ggugccguaacuucgggagaaggcacgcugauauguaggugaggucccuc
gcggauggagcugaaaucagucgaagauaccagcuggcugcaacuguuua
uuaaaaacacagcacugugcaaacacgaaaguggacguauacggugugac
gccugcccggugccggaagguuaauugaugggguuagcgcaagcgaagcu
cuugaucgaagccccgguaaacggcggccuaagguagcgaaauuccuugu
cggguaaguuccgaccugcacgaauggcguaaugauggccaggcugucuc
cacccgagacucagugaaauugaacucgcugugaagaugcaguguacccg
cggcaagacggaaagaccccgugaaccuuuacuauagcuugacacugaac
auguucuaacguugacccguaauccggguugcggacagugucuggugggu
aguuugacuggggcggucuccuccuaaagaguaacggaggagcacgaagg
uuggcuaauccggagguuagugcaauggcauaagccagcuugacugcgag
cgugacggcgcgagcaggugcgaaagcaggucauagugauccggugguuc
ugaauggaagggccaucgcucaacggauaaaagguacuccggggauaaca
ggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccucga
ugucggcucaucacauccuggggcugaaguaggucccaaggguauggcug
uucgccauuuaaagugguacgcgagcuggguuuagaacgucgugagacag
uucggucccuaucugccgugggcgcuggagaacugaggggggcugcuccu
aguacgagaggaccggaguggacgcaucacugguguucggguugucaugc
caauggcacugcccgguagcuaaaugcggaagagauaagugcugaaagca
ucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaaggg
uccugaaggaacguugaagacgacgacguugauaggccggguguguaagc
gcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaacc

<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<<..>>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<.<....<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>..>>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<<<..>>>
>>>>..>>>>...<............>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<......>>>>.>>>..>>.>.....
>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<......>>>>>>>>>
>....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<..
.........<<..<<<<<..<<................>>..>>>>>.>>
...........))).....>>>>>>.>>>...>>>>>>><<<<<......
>>>>>....>>>>>>..<<<<<...<<<......<<<<<<<<....>>>>
>>>>...>>>..>>>>>........>>>>>><......<<.....<<<<<
<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>
>.>>>>>>....((<<<.<<<...<<<...<<<....>>>...>>>...>
>>..<<<<<........>>>>>))<<<<<<<<<<<<<...<<<<....<<
<<..<<<..<<<<<<<<<<<....(((...>>>>>><<..<<<<...<<<
<<<<<<<<<.<<.....>>>>>>>>>>..>>>>...>>>>...>><..<<
<<<....>>>>>...>>>>>>...>>>...>>>>.........>>>>...
>>....>>>>>>>>>>>.>>>..>>.....<<......>>>>>>>.<<<<
.....>>>>..>>>>..<<<<....<<<<<<<<.<<..............
.<<<<<...............>>>>><<<<<<.....<<<...<<<<...
..>>>>...>>>...>>>>>>............<<<<<<<<<..<<<...
......>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<
<<<.<<<..<<<<<<<..<<<<...<...<<<<<..<<....>>...>>>
>>.>.....>>>>>>>>>..>>>>>...........<...........<<
<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>.....>>.
>>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<
<<<<.(((.[[......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<.
...>>>...<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>..>>
>>>..<<<<.....>>>><<<<<<...........>>>>>>.(<<...<<
<<<<<...<<..>>.....<<)..(((>>....>>>>>>>...<<<<..<
<<<....>>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.(
(..>>>>..))>>>>>>>.............>>>>..]]>>>>.......
<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>.....
..<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<..
...>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>
>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<.
..............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))
).>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<.......
....>>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....>>>
>><....<<..<<<<<.......>>>>>....<<<<<<<<..<<....<<
<<<....>>>>>...>>...>>>>>.>>>.....>>..>..>>>>>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cgk Structural conservation of antibiotic interaction with ribosomes.
• Resolution: 1.64 Å
• Binding residue (original residue number in PDB): L3 N4 L6 E10 G11 S12 K13 K14 G16 K17 R18 L19 G20 R21 G22 G24 S25 G28 K29 T30 G32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 R47 R48 F50 E51 G52 G53 Q54 M55 L57 Y58 R59 R60 L61 P62 K63 F64 G65 F66 S68 R69 A71 E76 R78 N99 I103 Q104 K109 I111 L112 T128 K129 G130
• Binding residue (residue number reindexed from 1): L3 N4 L6 E10 G11 S12 K13 K14 G16 K17 R18 L19 G20 R21 G22 G24 S25 G28 K29 T30 G32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 R47 R48 F50 E51 G52 G53 Q54 M55 L57 Y58 R59 R60 L61 P62 K63 F64 G65 F66 S68 R69 A71 E76 R78 N99 I103 Q104 K109 I111 L112 T128 K129 G130

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8cgk, PDBe:8cgk, PDBj:8cgk
• PDBsum: 8cgk
• PubMed: 37550453
• UniProt: P02413|RL15_ECOLI Large ribosomal subunit protein uL15 (Gene Name=rplO)